High-density deletion bin map of wheat chromosome 7B
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ABSTRACT:
PROVIDER: PRJNA246503 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Using 270K Nimblegen Comparative Genomic Hybridization (CGH) array on a set of cv. Chinese Spring deletion lines, a total of 3,671 sequence contigs and scaffolds (~7.8% of chromosome 7B physical length) were mapped into nine deletion bins. In our study we have developed 270K CGH Nimblegen array containing wheat 7B chromosome specific probes and genotyped wheat 7B deletion stocks which have terminal deletions in 7B. Our main aim was to identify absent probes (sequences) in deletion lines. Initially, spatial normalization and M-A loess normalization was performed for comparison test/reference and then clustering analysis (Mcust) was carried out. Further analysis was done on scaffolds (i.e. on larger sequences instead of probes; probes are designed from scaffolds)
2014-05-09 | GSE57461 | GEO
Project description:Using 270K Nimblegen Comparative Genomic Hybridization (CGH) array on a set of cv. Chinese Spring deletion lines, a total of 3,671 sequence contigs and scaffolds (~7.8% of chromosome 7B physical length) were mapped into nine deletion bins. In our study we have developed 270K CGH Nimblegen array containing wheat 7B chromosome specific probes and genotyped wheat 7B deletion stocks which have terminal deletions in 7B. Our main aim was to identify absent probes (sequences) in deletion lines. Initially, spatial normalization and M-A loess normalization was performed for comparison test/reference and then clustering analysis (Mcust) was carried out. Further analysis was done on scaffolds (i.e. on larger sequences instead of probes; probes are designed from scaffolds) Hybridization of DNA from 13 wheat lines, including 11 Chinese Spring cytogenetic stocks (Del7BL-9, DT7BL, DT7BS, Del7BL-13, Del7BL-14, Del7BL-5, Del7BL-1, Del7BL-7Del1DS-3, Del7BL-2,Del7BS-2, Del7BL-3) and 2 replicates of Langdon (LDN) tetraploid wheat. A set of 49,500 7B chromosome specific features (ISBP probes and random genomic features) and 18,000 control probes with each probe replicated four times on the 270K chip.
2014-05-09 | E-GEOD-57461 | biostudies-arrayexpress
Project description:A NimbleGen array containing both gene-based and RJM repeat junction probe sequences derived from Ae. Tauschii was developed and used to map the Chinese Spring nullisomic-tetrasomic lines and deletion bin lines of the D genome chromosomes.
2015-07-22 | GSE71190 | GEO
Project description:A NimbleGen array containing both gene-based and RJM repeat junction probe sequences derived from Ae. Tauschii was developed and used to map the Chinese Spring nullisomic-tetrasomic lines and deletion bin lines of the D genome chromosomes. The NimbleGen array was hybridized in duplicate with Cy3 labeled seven nullisomic-tetrasomic lines, deletion bin lines for D genome chromosomes, and control reference Chinese Spring; as well as Cy5 labeled reference line Chinese Spring.
2015-07-22 | E-GEOD-71190 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the following subset Series: GSE37360: Let-7b regulates skeletal muscle growth, development and fat deposition in deletion-type dwarf chickens (14-day-old embryos) GSE37367: Let-7b regulates skeletal muscle growth, development and fat deposition in deletion-type dwarf chickens (7-week-old chickens) Refer to individual Series
2012-04-17 | E-GEOD-37368 | biostudies-arrayexpress
Project description:Physiological changes underlying high density stress were examined in Oryza sativa plants over the course of a life cycle by assessing differences in gene expression. Moreover, the nitrogen limitation was examined in parallel with high density stress to gain a better understanding of physiological responses specific to high density stress. RNA was extracted from 21 and 31 days old plants. The plants were grown under four conditions: sufficient nitrogen (10mM N) and low density (six plants per bin), limiting nitrogen (3mM N) and low density, sufficient nitrogen and high density (40 plants per bin), limiting nitrogen and high density. Three biological replicates were sampled from each growth condition.
2014-08-24 | E-GEOD-57094 | biostudies-arrayexpress
Project description: Not available
| S-EPMC1448821 | biostudies-literature
Project description:A deletion mutation in the growth hormone receptor (GHR) gene results in the inhibition of skeletal muscle growth and fat deposition in dwarf chickens. In this study, microarray techniques were used to detect the miRNA and mRNA expression profiles of 14-day-old embryo and 7-week-old chicken skeletal muscle of deletion-type dwarf chickens and normal-type chickens. Skeletal muscle tissues of Dwarf recessive White Rock chickens and normal recessive White Rock chickens were used to make the microarray assay. Results show the expression of miR-1623 and miR-181b in 14-day-old embryos and of let-7b and miR-128 in 7-week-old chickens. let-7b was the only miRNA found to be completely complementary to its target in the 3'UTR of GHR and inhibited GHR gene expression. KEGG (Kyoto Encyclopaedia of Genes and Genomes) pathway analysis and RT-PCR verified that there were three main signalling pathways regulating the skeletal muscle growth and fat deposition of chickens influenced by the let-7b-regulated GHR gene. The suppression of the cytokine signalling 3 (SOCS3) gene was found to be involved in the signalling pathway of adipocytokines. We found that let-7b is the critical miRNA involved in the regulation of the GHR gene. SOCS3 plays a critical role in the network regulating skeletal muscle growth and fat deposition via let-7b-mediated GHR gene expression.
2012-04-18 | GSE37367 | GEO
Project description:A deletion mutation in the growth hormone receptor (GHR) gene results in the inhibition of skeletal muscle growth and fat deposition in dwarf chickens. In this study, microarray techniques were used to detect the miRNA and mRNA expression profiles of 14-day-old embryo and 7-week-old chicken skeletal muscle of deletion-type dwarf chickens and normal-type chickens. Skeletal muscle tissues of Dwarf recessive White Rock chickens and normal recessive White Rock chickens were used to make the microarray assay. Results show the expression of miR-1623 and miR-181b in 14-day-old embryos and of let-7b and miR-128 in 7-week-old chickens. let-7b was the only miRNA found to be completely complementary to its target in the 3'UTR of GHR and inhibited GHR gene expression. KEGG (Kyoto Encyclopaedia of Genes and Genomes) pathway analysis and RT-PCR verified that there were three main signalling pathways regulating the skeletal muscle growth and fat deposition of chickens influenced by the let-7b-regulated GHR gene. The suppression of the cytokine signalling 3 (SOCS3) gene was found to be involved in the signalling pathway of adipocytokines. We found that let-7b is the critical miRNA involved in the regulation of the GHR gene. SOCS3 plays a critical role in the network regulating skeletal muscle growth and fat deposition via let-7b-mediated GHR gene expression.
2012-04-18 | GSE37360 | GEO
Project description:A deletion mutation in the growth hormone receptor (GHR) gene results in the inhibition of skeletal muscle growth and fat deposition in dwarf chickens. In this study, microarray techniques were used to detect the miRNA and mRNA expression profiles of 14-day-old embryo and 7-week-old chicken skeletal muscle of deletion-type dwarf chickens and normal-type chickens. Skeletal muscle tissues of Dwarf recessive White Rock chickens and normal recessive White Rock chickens were used to make the microarray assay. Results show the expression of miR-1623 and miR-181b in 14-day-old embryos and of let-7b and miR-128 in 7-week-old chickens. let-7b was the only miRNA found to be completely complementary to its target in the 3'UTR of GHR and inhibited GHR gene expression. KEGG (Kyoto Encyclopaedia of Genes and Genomes) pathway analysis and RT-PCR verified that there were three main signalling pathways regulating the skeletal muscle growth and fat deposition of chickens influenced by the let-7b-regulated GHR gene. The suppression of the cytokine signalling 3 (SOCS3) gene was found to be involved in the signalling pathway of adipocytokines. We found that let-7b is the critical miRNA involved in the regulation of the GHR gene. SOCS3 plays a critical role in the network regulating skeletal muscle growth and fat deposition via let-7b-mediated GHR gene expression. Two groups were analyzed in the array assay: one group consisted of normal recessive White Rock 14-day-old embryo leg muscle tissues, and the other group consisted of dwarf recessive White Rock 14-day-old embryo leg muscle tissues. The control samples were labeled as A1, A2, A3, and the dwarf chicken samples were labeled as B1, B2, and B3. 9 total embryos per breed, 3 embryos used per breed for each sample. 523 mature miRNA sequences were assembled and integrated into the LC miRNA microarray design, and different expression miRNAs were measured on the 7000HT Fast Real-Time PCR system. This submission represents the miRNA profiling component of the study.
2012-04-17 | E-GEOD-37360 | biostudies-arrayexpress